diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..47dbe4b --- /dev/null +++ b/Dockerfile @@ -0,0 +1,83 @@ +# Base Image +FROM ncbihackathon/ncbihackathonbase:latest + +# Metadata +LABEL base.image="ncbihackathonbase:latest" +LABEL version="1" +LABEL software="NCBI Hackathon Image for NGS analysis" +LABEL software.version="0.0.1" +LABEL description="NCBI Hackathons Image for NGS analysis" +LABEL website="https://github.com/NCBI-Hackathons/HackathonDockerImages/Docker/ngs" +LABEL documentation="https://github.com/NCBI-Hackathons/HackathonDockerImages/Docker/ngs" +LABEL license="https://github.com/NCBI-Hackathons/HackathonDockerImages/LICENSE" +LABEL tags="NCBI, Hackathon, Bioconductor" + +# Maintainer +MAINTAINER Roberto Vera Alvarez + +USER biodocker + +RUN git clone --recursive https://github.com/NCBI-Hackathons/NanoporeMapper.git + +# Samtools 1.6 +ENV ZIP=samtools-1.6.tar.bz2 +ENV URL=https://github.com/samtools/samtools/releases/download/1.6/ +ENV FOLDER=samtools-1.6 +ENV DST=/tmp + +RUN wget $URL/$ZIP -O $DST/$ZIP && \ + tar xvf $DST/$ZIP -C $DST && \ + rm $DST/$ZIP && \ + cd $DST/$FOLDER && \ + ./configure --prefix=/home/biodocker && \ + make && \ + make install && \ + cd / && \ + rm -rf $DST/$FOLDER + +# BAMTools 2.5.1 +ENV ZIP=v2.5.1.tar.gz +ENV URL=https://github.com/pezmaster31/bamtools/archive/ +ENV FOLDER=bamtools-2.5.1 +ENV INSTALL_FOLDER=/home/biodocker/ +ENV DST=/tmp +ENV LD_LIBRARY_PATH=$INSTALL_FOLDER/lib/bamtools:$LD_LIBRARY_PATH + +RUN cd $DST && \ + wget $URL/$ZIP -O $DST/$ZIP && \ + tar xzfv $DST/$ZIP -C $DST && \ + cd $DST/$FOLDER && mkdir build && cd build && \ + cmake -DCMAKE_INSTALL_PREFIX=$INSTALL_FOLDER .. && make && \ + make install && \ + rm -rf $DST/$FOLDER $DST/$ZIP + +# STAR 2.5.3a +ENV ZIP=2.5.3a.tar.gz +ENV URL=https://github.com/alexdobin/STAR/archive/ +ENV FOLDER=STAR-2.5.3a +ENV INSTALL_FOLDER=/home/biodocker/ +ENV DST=/tmp + +RUN cd $DST && \ + wget $URL/$ZIP -O $DST/$ZIP && \ + tar xzfv $DST/$ZIP -C $DST && \ + cd $DST/$FOLDER/source && \ + make && \ + mv STAR /home/biodocker/bin/ && \ + rm -rf $DST/$FOLDER $DST/$ZIP + +# NCBI-magicblast 1.3.0 +ENV ZIP=ncbi-magicblast-1.3.0-x64-linux.tar.gz +ENV URL=ftp://ftp.ncbi.nlm.nih.gov/blast/executables/magicblast/1.3.0/ +ENV FOLDER=ncbi-magicblast-1.3.0 +ENV INSTALL_FOLDER=/home/biodocker/ +ENV DST=/tmp + +RUN cd $DST && \ + wget $URL/$ZIP -O $DST/$ZIP && \ + tar xzfv $DST/$ZIP -C $DST && \ + mv $DST/$FOLDER/LICENSE $DST/$FOLDER/README /home/biodocker/bin/ && \ + mv $DST/$FOLDER/bin/* /home/biodocker/bin/ && \ + rm -rf $DST/$FOLDER + +WORKDIR /data/